Summary stats

General stats about the patient cohort

Stat	Value
Unique HPO terms	24
Cohort size	3971
Rejected patients by empty profile	0
HPOs per patient (average)	2.7107
HPO terms per patient: percentile 90	1
Percentage of HPO with more specific children	81.7168
DsI for uniq HP terms	0
DsI for frequency weigthed HP terms	0
Number of unknown phenotypes	0
Number of clusters with mutations accross > 1 chromosomes	2891
Average variant size	4210308.4241
Nucleotides affected by mutations	1728337900
Number of genome windows	1597
Mean patients per genome window	3.9818
Number of genome window shared by >= 2 patients	1097
Number of patients with at least 1 SOR	1027
Nucleotides affected by mutations	974263470

HPO stats

HPOs more frequent in the cohort

HPO	Patient percentage
Cognitive impairment	80.96197431377486
Intellectual disability, mild	17.678166708637622
Short stature	17.325610677411234
Autistic behavior	16.872324351548727
Hypotonia	15.361369932007051
Intellectual disability, severe	15.26063963737094
Seizure	15.23545706371191
Behavioral abnormality	13.220851170989675
Microcephaly	12.465373961218837
Intellectual disability, moderate	11.004784688995215
Morphological central nervous system abnormality	8.562075044069504
Intrauterine growth retardation	8.335431881138252
Abnormal external genitalia	6.698564593301436
Attention deficit hyperactivity disorder	5.615713925963233
Macrocephaly	4.960967010828507
Abnormal cardiac septum morphology	4.230672374716696
Abnormality of the upper urinary tract	3.9032989171493324
Conotruncal defect	3.2485520020146064
Tall stature	2.719717955175019
Abnormality of cardiovascular system morphology	2.3419793502896
Abnormal heart valve morphology	2.316796776630572
Abnormality of the lower urinary tract	2.039788466381264
Abnormal internal genitalia	0.4281037522034752
Abnormality of the genitourinary system	0.2770083102493075

Cohort genome coverage analysis

Distribution of the genome coverage of all mutations characterized in the cohort. Second figure shows the same results for SORs.

HPO annotations distribution

Analysis of the HPO terms within the HPO ontology and the cohort of patients. Left: distribution of terms within the ontology and the cohort. Right: percentage of terms distribution within the ontology and the cohort.

HPOs frequency distribution. Colour based on the HPO frequency.

Clustering patients by HPO profile

All patients are clustered using their HPO profiles. First figure shows the information coefficient distribution for the top clusters. Second figure shows which chromosomes are affected in the patients for each top cluster.

HPO profile redundancy

For each patient profile size (number of phenotypes, x-axis) it is shown the number of HPO phenotypes that are parent of other terms within the profile (number of parent terms, y-axis).

HPO ICs distribution

First figure shows the ICs distribution in terms of the HP ontology (x-axis) and for each single HPO term, its frequency in the cohort according to the HP ontology structure (y-axis) and the second figure shows the same distributions considering the profiles analyzed.

HPO frequency by cluster

Patients in Cluster 0	Phenotypes	Frequency
688	Cognitive impairment	100.0

Patients in Cluster 1	Phenotypes	Frequency
137	Cognitive impairment, Intellectual disability, mild	100.0, 100.0

Patients in Cluster 2	Phenotypes	Frequency
106	Cognitive impairment, Autistic behavior	100.0, 100.0

Patients in Cluster 3	Phenotypes	Frequency
80	Cognitive impairment, Behavioral abnormality	100.0, 100.0

Patients in Cluster 4	Phenotypes	Frequency
71	Cognitive impairment, Intellectual disability, moderate	100.0, 100.0

Patients in Cluster 5	Phenotypes	Frequency
66	Cognitive impairment, Intellectual disability, mild, Autistic behavior	100.0, 100.0, 100.0

Patients in Cluster 6	Phenotypes	Frequency
63	Cognitive impairment, Intellectual disability, mild, Behavioral abnormality, Abnormal cardiac septum morphology, Abnormality of the genitourinary system	100.0, 100.0, 100.0, 1.5873, 1.5873

Patients in Cluster 7	Phenotypes	Frequency
62	Short stature	100.0

Patients in Cluster 8	Phenotypes	Frequency
60	Cognitive impairment, Seizure	100.0, 100.0

Patients in Cluster 9	Phenotypes	Frequency
48	Behavioral abnormality	100.0

Patients in Cluster 10	Phenotypes	Frequency
47	Cognitive impairment, Short stature	100.0, 100.0

Patients in Cluster 11	Phenotypes	Frequency
47	Cognitive impairment, Intellectual disability, severe	100.0, 100.0

Patients in Cluster 12	Phenotypes	Frequency
45	Cognitive impairment, Hypotonia	100.0, 100.0

Patients in Cluster 13	Phenotypes	Frequency
41	Cognitive impairment, Intellectual disability, moderate, Autistic behavior	100.0, 100.0, 100.0

Patients in Cluster 14	Phenotypes	Frequency
40	Autistic behavior	100.0

Patients in Cluster 15	Phenotypes	Frequency
39	Cognitive impairment, Intellectual disability, severe, Autistic behavior	100.0, 100.0, 100.0

Patients in Cluster 16	Phenotypes	Frequency
38	Morphological central nervous system abnormality	100.0

Patients in Cluster 17	Phenotypes	Frequency
38	Abnormality of cardiovascular system morphology, Behavioral abnormality	100.0, 2.6316

Patients in Cluster 18	Phenotypes	Frequency
33	Hypotonia	100.0

Patients in Cluster 19	Phenotypes	Frequency
31	Abnormality of the upper urinary tract	100.0

Patients in Cluster 20	Phenotypes	Frequency
30	Cognitive impairment, Intellectual disability, mild, Short stature	100.0, 100.0, 100.0

Patients in Cluster 21	Phenotypes	Frequency
27	Cognitive impairment, Microcephaly	100.0, 100.0

Patients in Cluster 22	Phenotypes	Frequency
26	Cognitive impairment, Intellectual disability, severe, Seizure, Abnormal internal genitalia, Abnormal cardiac septum morphology	100.0, 100.0, 100.0, 3.8462, 3.8462

Patients in Cluster 23	Phenotypes	Frequency
25	Microcephaly	100.0

Patients in Cluster 24	Phenotypes	Frequency
25	Cognitive impairment, Intellectual disability, severe, Behavioral abnormality, Abnormal internal genitalia	100.0, 100.0, 100.0, 4.0

Patient profiles heatmaps

For each patient, their HPO profile similarity coefficient is calculated according to the different methods specified in the analysis and represented in these heatmaps.